source: NEMO/branches/2018/dev_r9866_HPC_03_globcom/cfgs/AGRIF_DEMO @ 10289

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EXPREF 10289   3 years francesca alignment to the current version of the trunk
MY_SRC 9787   3 years clem set nbghostcells=3 by default instead of 1. The nesting tools are already …
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README.rst 4.5 KB 10289   3 years francesca alignment to the current version of the trunk
zooms.bib 1.4 KB 10289   3 years francesca alignment to the current version of the trunk


Embedded zooms (AGRIF)

.. contents::


AGRIF (Adaptive Grid Refinement In Fortran) is a library that allows the seamless space and time refinement over
rectangular regions in NEMO.
Refinement factors can be odd or even (usually lower than 5 to maintain stability).
Interaction between grid is "two-ways" in the sense that the parent grid feeds the child grid open boundaries and
the child grid provides volume averages of prognostic variables once a given number of time step is completed.
These pages provide guidelines how to use AGRIF in NEMO.
For a more technical description of the library itself, please refer to


Activating AGRIF requires to append the cpp key ``key_agrif`` at compilation time: 

.. code-block:: sh

   ./makenemo add_key 'key_agrif'

Although this is transparent to users, the way the code is processed during compilation is different from
the standard case:
a preprocessing stage (the so called "conv" program) translates the actual code so that
saved arrays may be switched in memory space from one domain to an other.

Definition of the grid hierarchy

An additional text file ```` is required at run time.
This is where the grid hierarchy is defined.
An example of such a file, here taken from the ``ICEDYN`` test case, is given below::

   34 63 34 63 3 3 3

The first line indicates the number of zooms (1).
The second line contains the starting and ending indices in both directions on the root grid
(imin=34 imax=63 jmin=34 jmax=63) followed by the space and time refinement factors (3 3 3).
The last line is the number of child grid nested in the refined region (0).
A more complex example with telescoping grids can be found below and
in the ``AGRIF_DEMO`` reference configuration directory.

[Add some plots here with grid staggering and positioning ?]

When creating the nested domain, one must keep in mind that the child domain is shifted toward north-east and
depends on the number of ghost cells as illustrated by the (attempted) drawing below for nbghostcells=1 and
The grid refinement is 3 and nxfin is the number of child grid points in i-direction.  

.. image:: _static/agrif_grid_position.jpg

Note that rectangular regions must be defined so that they are connected to a single parent grid.
Hence, defining overlapping grids with the same refinement ratio will not work properly,
boundary data exchange and update being only performed between root and child grids.
Use of east-west periodic or north-fold boundary conditions is not allowed in child grids either.
Defining for instance a circumpolar zoom in a global model is therefore not possible. 


Knowing the refinement factors and area, a ``NESTING`` pre-processing tool may help to create needed input files
(mesh file, restart, climatological and forcing files).
The key is to ensure volume matching near the child grid interface,
a step done by invoking the ``Agrif_create_bathy.exe`` program.
You may use the namelists provided in the ``NESTING`` directory as a guide.
These correspond to the namelists used to create ``AGRIF_DEMO`` inputs.

Namelist options

Each child grid expects to read its own namelist so that different numerical choices can be made
(these should be stored in the form ``1_namelist_cfg``, ``2_namelist_cfg``, etc... according to their rank in
the grid hierarchy).
Consistent time steps and number of steps with the chosen time refinement have to be provided.
Specific to AGRIF is the following block:

.. code-block:: fortran

   &namagrif      !  AGRIF zoom                                            ("key_agrif")
      ln_spc_dyn    = .true.  !  use 0 as special value for dynamics
      rn_sponge_tra = 2880.   !  coefficient for tracer   sponge layer [m2/s]
      rn_sponge_dyn = 2880.   !  coefficient for dynamics sponge layer [m2/s]
      ln_chk_bathy  = .false. !  =T  check the parent bathymetry

where sponge layer coefficients have to be chosen according to the child grid mesh size.
The sponge area is hard coded in NEMO and applies on the following grid points:
2 x refinement factor (from i=1+nbghostcells+1 to i=1+nbghostcells+sponge_area) 


.. bibliography:: zooms.bib
   :style: unsrt
   :labelprefix: A
   :keyprefix: a-
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